RaverJay

Does the Pseudo-fusion filter discard chimeric reads completely?

2

Hey, see title. Also, is it not feasible to split the read und process/keep both fused reads? Cheers

Trimgalore -> cutadapt -> OSError: [Errno 40] Too many levels of symbolic links

1

### Description of the bug Running rnaseq -r 3.8.1 with -profile docker on a local machine gives this strange error that has me stumped. "Too many levels of symbolic links"...

Why are signal lengths per nucleotide always multiples of 12?

3

Hey there, I noticed the signal lengths for each nucleotide are only multiples of 12 after re-squiggling with prepare_mapped_reads.py So differences between adjacent values in Ref_to_signal are e.g. [ 24.,...

Idea for the report table: A mini-plot that shows where Ns are in the assemblies

14

Could also include warnings when N stretches are in important regions, e.g. the spike protein As any mutations/deletions/insertions are just omitted when the corresponding region isn't covered enough, this might...